Hit 'in' or hit 'on' (one's head)

You can say either:

I hit him on the head.

This implies that you hit him on the top of the head, or skull.

I hit him in the head.

This implies that you hit him somewhere in the head, but not necessarily on top.

Look at the headline here which uses "hit in the head":

http://www.myfoxboston.com/dpp/news/offbeat/justin-bieber-hit-in-the-head-with-water-bottle-20100809

I agree with Robusto. You ask for other ways to ask that question. I would naturally say:

Ohhh, did you hit your head?

Without prepositions, "Hit your head" means roughly the same as "Hit in the head". The difference is that "Hit in the head" means it came from external sources, like someone throwing a ball at you. "Hit your head" just means your head was hit, with no implication of the source / fault.

I would always use "on" for a blow to a body part, unless the body part I was literally referring to was an internal organ, or otherwise regarded as interior. So "on the head", "on the arm", "on the back", but "in the kidneys", "in the belly", and "in the crotch".

If I heard "hit in the head" I would think first of a gunshot wound rather than a blow.

Both are common usage in the UK:

'in' is often used in the sense of "in the region of" or "in the area (location)" of the head. It is not used literally to mean "inside of" or within.

Both "Did the ball hit you on the head?" and "Did the ball hit you in the head" are equally valid.

IN is normally used when you need to indicate a position for spaces with limitations OR to convey either something that is contained within or inside something else. "In the head", in this case indicates a limitation of geography [physiology] rather than containment inside something else - a ball inside the person's skull, although it could be used in this sense "Have you got a ball in your head?!".

Alternatively, ON is normally used to denote a position in relation to a surface or a position just above or outside an area.

Mine eyes have seen the glory of the burning of the school, We've terrorised the teachers, And we've broken every rule! We have bound and gagged the principal And tossed him in the pool The school is burning down. Rah! Rah! Rah!

Glory, glory halleluja, teacher hit me with a ruler I bopped her on the bean with a rotten tangerine And her teeth came marching out! Chatter, Chatter!